Furlong was much more successful at Watford in Division One (the new name for the original Second Division after the creation of the Premier League), and was voted Watford Player of the Season in 1993. Although he failed to inspire Watford to a promotion challenge, he established himself as one of the finest strikers in the division at this time, alongside the likes of Steve Bull and Stan Collymore.

At the end of the 1993–94 season, he became Chelsea's record signing in a £2.3million deal, and that season he helped them reach the UEFA Cup Winners' Cup semi-finals (losing to Real Zaragoza by a single goal) as well as finish 11th in the Premier League. However, the arrival of Ruud Gullit and Mark Hughes during the 1995 close season reduced his first team opportunities, and following the arrival of Gianluca Vialli a year later he opted to move on. During his time at Chelsea he scored 18 goals in 85 matches in all competitions.

He finally left the Blues in the summer of 2002, the year they reached the Premier League after 16 years outside the top flight, and signed a contract with Queen's Park Rangers in Division Two. This was a return to a previous club as Furlong had been a youth team player at QPR at the start of his career. He continued to do well at Loftus Road, helping them win promotion in 2004, and by the time he left in 2007, he had played 162 league games and scored 54 goals.

On leaving QPR, the 38-year-old Furlong signed for Luton Town who had just been relegated from the Football League Championship. He scored eight goals in 32 games but was unable to prevent the financially troubled side from suffering a second successive relegation.

He then signed for League One side Southend United, but made just 3 appearances during the first half of the season and was loaned out to Barnet in January 2009.[3] After two goals in January the loan spell was extended until the end of the season. His goal in Barnet's 1–0 win against AFC Bournemouth was his 200th senior goal, and he marked the occasion by laying down his shirt and saluting it.[4]

He was released by Southend at the end of the 2008–09 season, and joined Barnet on a one-year deal after an excellent pre-season This was subsequently extended until the end of the 2009–10 season. On 2 June 2010, Furlong was released by Barnet.